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Name: EDAMontology

Type: Organization

Bio: EDAMontology is an umbrella organisation for the development and maintenance of the EDAM ontology and related tools and works.

Twitter: edamontology

Blog: http://edamontology.org

DOI representing all stable versions, resolving to the latest:

DOI of the latest stable EDAM version 1.25:

Current status of the 'main' development file:

Latest documentation:

Twitter: @edamontology (follow).

What is EDAM?

EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use (see figure).

EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to bioscientific data analysis: e.g. tools, workflows, or training materials. EDAM is also useful in data management, for recording provenance metadata of processed bioscientific data.

Viewing and download

EDAM can be browsed online at the NCBO BioPortal, at OLS, and in the EDAM Browser.

The all-newest unstable version can be browsed and commented at the NCBO BioPortal and WebProtégé (free registration required).

The latest stable version is always downloable from http://edamontology.org/EDAM.owl | tsv | csv. For older versions, see http://edamontology.org/page#Download or /releases.

Documentation

Comprehensive documentation and guidelines are available via readthedocs (maintained here).

A quick overview is at the http://edamontology.org home page.

Citing EDAM

If you refer to EDAM or its part in a scholarly publication, please cite:

Melissa Black, Lucie Lamothe, Hager Eldakroury, Mads Kierkegaard, Ankita Priya, Anne Machinda, Uttam Singh Khanduja, Drashti Patoliya, Rashika Rathi, Tawah Peggy Che Nico, Gloria Umutesi, Claudia Blankenburg, Anita Op, Precious Chieke, Omodolapo Babatunde, Steve Laurie, Steffen Neumann, Veit Schwämmle, Ivan Kuzmin, Chris Hunter, Jonathan Karr, Jon Ison, Alban Gaignard, Bryan Brancotte, Hervé Ménager, Matúš Kalaš (2022). EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]. F1000Research, 11(ISCB Comm J): 1. Poster. Open access

EDAM releases are citable with DOIs too, for cases when that is needed. represents all releases and resolves to the DOI of the last stable release.

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit our informational page or download our participant information sheet.

License

EDAMontology's Projects

benten

A language server for Common Workflow Language

caseologue

Validation tools for the EDAM ontology

debtag2edam2debtags

The EDAM ontology for bioinformatics tools and services should be come compatible with the Debtags and vice versa. This project starts out with adding EDAM references to the debtags volcabulary export file.

edam-bioimaging

Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..

edam-browser

Stand-alone, lightweight, and fast JavaScript browser for EDAM and other ontologies

edam-geo

Extension of EDAM towards geo- and other sciences, including Earth and planetary sciences, climate science, ecology, public health, environmental monitoring, emergency management, etc. Everyone welcome to view & comment at https://webprotege.stanford.edu/#projects/69591619-4eda-4f03-9e7f-65b213038fe1/edit/Classes (free registration needed).

edam-geo-test.bak

Extension of the EDAM ontology for geo-related concepts, including areas of Earth and planetary sciences, climate research, ecology, public health, etc.

edam-geo-wp-dump

EDAM ("Geo"), raw download from WebProtégé

edam-ontology.py

edam-playground

Slides, swings, and sandbox ontology

edam-popovers

A Firefox & Chrome extension that displays detailed information about EDAM concepts

edam-stub-experiment

edam2json

utility to export EDAM to various sorts of JSON formats (JSON-LD, bio.tools JSON)

edam2json-js

Javascript library to convert EDAM to JSON/JSON-LD

edammap

A tool for mapping various text input to EDAM ontology concepts

edamontology

EDAM is an ontology of bioscientific data analysis and data management. EDAM concentrates on topics, operations, types of data, and data formats related to analysis, modelling, optimisation, and data life-cycle in biosciences, and in other research and science-based applications.